This data set gives an example of a protein alignment obtained after a call to the function read.alignment on an alignment file in "clustal" format.
clustalA List of class alignment
Thompson, J.D., Higgins D.G., Gibson T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22):4673-80.